Y. Yamagata

Diketopiperazine-mediated peptide formation in aqueous solution

Though diketopiperazines (DKP) are formed in most experiments concerning the prebiotic peptide formation, the molecules have not been paid attention in the studies of chemical evolution. We have found that triglycine, tetraglycine or pentaglycine are formed in aqueous solution of glycine anhydride (DKP) and glycine, diglycine or triglycine, respectively. A reaction of alanine with DKP resulted in the formation of glycylglycylalanine under the same conditions. These results indicate that the formation of the peptide bonds proceeds through the nucleophilic attack of an amino group of the amino acids or the oligoglycines on the DKP accompanied by the ring-opening.The formation of glycine anhydride, di-, tri- and tetraglycine was also observed in a mixed aqueous solution of urea and glycine in an open system to allow the evaporation of ammonia. A probable pathway is proposed for prebiotic peptide formation through diketopiperazine on the primitive Earth.

Condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solutions

The dehydration condensation of glycine with trimetaphosphate in aqueous solution has been reinvestigated. Although it has been reported that the condensation of glycine under the alkaline conditions was brought about through the formation of cyclic acylphosphoramidate and hence the condensation of polyglycines could not occur, we found that the condensation of oligoglycines with trimeta- and tetrametaphosphate in aqueous solution are possible through the formation of their acylphosphates under the neutral or weak acidic conditions.Aqueous solutions of 1.0 M glycylglycine and 1.0 M trimetaphosphate in the various pH from 4.0 to 9.0 were incubated at 38 °C. The solutions were analyzed by HPLC with ninhydrin reaction system. Tetraglycine and hexaglycine were detected and their maximum yields were given in the reaction carried out around pH 7. They are approximately 15% and 4% after 30 days, respectively. Analogous experiments were performed with tetrametaphosphate. The results showed a similar pH dependence for the condensation, but the yields were about one-tenth of those of corresponding experiments with trimetaphosphate.Relative rates of dimerization of glycine, diglycine and triglycine in the equimolar concentration were also investigated at pH 6.0 at 38 °C. The rates for digylcine and triglycine were approximately twice and four times as large as that for glycine.Relevance of the experiments to chemical evolution is discussed.

PREBIOTIC FORMATION OF ADP AND ATP FROM AMP, CALCIUM PHOSPHATES AND CYANATE IN AQUEOUS SOLUTION

Adenosine-5′-triphosphate was synthesized by the phosphorylation of adenosine-5′-diphosphate in aqueous solution containing cyanate as a condensing reagent and insoluble calcium phosphate produced from phosphate and calcium chloride. In a similar manner, adenosine-5′-diphosphate was synthesized from adenosine-5′-monophosphate. When the experiment was carried out in the conditions of 4 °C and pH 5.75, the formation of adenosine-5′-diphosphate and adenosine-5′-triphosphate from adenosine-5′-monophosphate was observed in the yields of 19 and 7%, respectively. The other nucleoside-5′-triphosphates were also produced from their respective diphosphates.

FORMATION OF CYANATE AND CARBAMYL PHOSPHATE BY ELECTRIC DISCHARGES OF MODEL PRIMITIVE GAS

A mixed gas of nitrogen, carbon dioxide, and hydrogen was discharged over 100 ml of 0.2M NaHCO3 solution in a 5 liter discharge apparatus which simulates the primitive Earth. The formation of cyanate, which is one of the possible primitive condensing agents, was demonstrated by the detection of [Cu(Py)2] (NCO)2 that was formed by the addition of copper sulfate-pyridine reagent to the solution. In a series of experiments the partial pressures of nitrogen and carbon dioxide in the starting gas were fixed at 10 cm Hg and 20 cm Hg, respectively, whereas that of hydrogen was varied between 5, 10, 15, 20, 25, and 30 cm Hg. The discharges were continued for one week. The rate of appearance of cyanate was strongly dependent upon the partial pressure of hydrogen. The maximum rate of the production of cyanate at the initial stage of the discharge was in the case of 10 cm Hg of hydrogen, in which condition the starting gas is in a predominantly oxidized state. In this case the concentration of cyanate reached about 0.012M after one day. Another discharge experiment was carried out with 0.2M phosphate solution, and the production of carbamyl phosphate was demonstrated through the formation of ATP by the incubation of the discharged solution with ADP and carbamyl phosphokinase.

AMP synthesis in aqueous solution of adenosine and phosphorus pentoxide

Possible formation of a P4O10 molecule in magma, the stability of the molecule in hydrous volcanic gas at high temperatures and a possible prebiotic phosphate cycle were discussed in relation to chemical evolution. To demonstrate the utility of phosphorus pentoxide as a phosphorylating agent, aqueous solutions of adenosine (0.02M) and phosphorus pentoxide (0.2M) were incubated at 37°C for 5 months. The pH of the solutions was adjusted every day or every few days to each fixed value (9.0, 10.5, 11.5, 12.5) with 10 N NaOH. The HPLC analysis showed the formation of 2′-AMP, 3′-AMP, 5′-AMP, cyclic (2′–3′)-AMP and cyclic (3′–5′)-AMP. The main components of the products were 2′- and 3′-AMP, though cyclic (2′–3′)-AMP was the main component in the early period of the incubation at pH 9.0. The yields (conversion rate of adenosine to AMPs) were increased almost linearly with the incubation time for 5 months in the case of pH 9.0. The final yields were about 3% (pH 9.0), 6% (pH 9.0, 1 M NaCl), 5% (pH 9.0, 0.01 M CaCl2, 0.01 M MgCl2), 7% (pH 9.0, 0.5 M NaCl, 0.01 M CaCl2, 0.01 M MgCl2), 9% (pH 9.0, 1 M NaCl, 0.01 M CaCl2, 0.01 M MgCl2), 32% (pH 10.5), 43% (pH 11.5), 35% (pH 12.5).

Synthesis of biomolecules from N2, CO, and H2O by electric discharge

A model primitive gas containing a mixture of N2, CO and water vapor over a water pool (300 mL, ∼ 37 °C) was subjected to electric discharges. The discharge vessel (7 L in volume) was equipped with a CO2 absorber (The CO2 being formed during the discharge), thus simulating possible absorption of CO2 in the primitive ocean. The vessel also has a cold trap (∼ −15 °C), which protects the primary products against the further decomposition in the discharge phase by enabling these products to adhere to the trap. Since the partial pressures of CO and N2 decreased at rates of 1.5–1.7 cmHg day−1 and 0.1–0.2 cmHg day−1, respectively, the gases were added at regular intervals. The solution was analyzed at regular intervals for HCN, HCHO and urea, and maximum concentrations of about 50, 2, and 140 mM were observed. The discharge phase was continued for 6 months. In the solution, glycine (5.6% yield based on the carbon), glycylglycine (0.64%), orotic acid (0.004%) and small amounts of the other amino acids were found.

Prebiotic synthesis of orotic acid parallel to the biosynthetic pathway

By heating an aqueous solution of aspartic acid and urea, carbamylaspartic acid is first formed and then the molecule is cyclized to dihydroorotic acid (DHO) with loss of water. Irradiation of an aqueous solution of DHO with a tungsten lamp yields orotic acid by photo-dehydrogenation of the molecule. This pathway of orotic acid formation is quite similar to that of biosynthesis of the molecule.

Constant AMP synthesis in aqueous solution by electric discharges

An electric discharge was made through a gas mixture of N2 (7 cm Hg), H2 (14 cm Hg) and CO2 (14 cm Hg) over an aqueous solution (100 ml, pH 7.6) of adenosine (0.02 M) and phosphate (0.2 M) in a 5 liter vessel simulating primitive earth conditions. AMP was produced at a constant rate in the solution, and the yield reached about 2% in two months.

Diketopiperazine-mediated peptide formation in aqueous solution II. Catalytic effect of phosphate

The previous paper (I) reported that DKP (glycine anhydride) spontaneously reacts with glycine (Gly) or oligoglycines (Glyn) to produce longer oligoglycines (Glyn+2). This paper presents that phosphate catalyzes the condensation reaction quite effectively.Formation of Gly4 from DKP (0.1 M) and Gly2 (0.1 M) in phosphate solution of various concentrations was investigated at a neutral pH at 41 °C. The yields of Gly4 increased almost linearly with the concentration of phosphate from 0.06 M to 0.24 M. The yield in 0.24 M phosphate solution was approximately one hundred times as high as that in the absence of the phosphate, whereas in the case of Gly3 formation from DKP and Gly the effect of the phosphate was of ten times lower than in the former case. Orthophosphate was the most effective catalyst among the various kind of chemicals tried in the present investigation including polyphosphates.

Computer experiment for selection of optical isomer during prebiotic polymerization

Computer experiments simulating prebiotic polymerization were carried out using the Monte Carlo method. A high degree of selection of single optical isomers from racemic monomers occurred by assuming a small asymmetry in their chemical natures, which was included to investigate an, amplification of the asymmetry due to parity non-conservation. The asymmetry developed much more slowly than the growth of polymers, and the degree of asymmetry in the polymers increased with the degree of polymerization. Competition between the preferential selection and the disturbance by the statistical fluctuation are discussed.